We found a couple of pub-restaurants near the centre of Prague that were not touristic, the food was traditional and prices were not inflated. I can't remember their names! But here's where they are: In Wenceslas square go nearly to the Muzeum at one end. Take the last turning on the right, the pub is 20 or 30 metres on the left. On the metro yellow line, travel one stop west of Mustek. The station name escapes me. Tesco supermarket adjoins the station on one side, and toilets on another side. With your back to the toilets the restaurant entrance is on the other side of the street with a little arch over the door. It doesn't look as though there's a restaurant there. You go through the door and down some stairs to find it. Pork knee was great. But check your bill carefully. We did and found we had been seriously overcharged!
Is that just down the street from Agharta jazz club? I've been there a few times. It's great! Oops! Just looked, and Agharta has moved now to Zelezna.
My Czech friends like U Milosrdnych, U Milosrdnych 12, Stare Mesto. I don't know if it is "non-touristic," but it is cheap and good, especially for being so near the center.